I think all the references to the online source of the toilet have kept some participants away; we don't usually talk about online sources here, but I'm happy to answer your questions.
Usually, we recommend flange spacers under the flange not the ones that go over, unless you really caulk the heck out of the spaces in-between, and usually not even then. Better off with double wax rings in that case, or double sani-seals, etc.
Are you measuring the rough-in to the finished wall, not the baseboard? If so, and you really have a full 11", the toilet you reference SHOULD just fit, because there is usually 1-1/8" behind it when installed on exactly 12". However, if your wall isn't exactly vertical and thus it's a little less than 11", it might not go. It's a risk you can take, and probably succeed, but we're talking eighths of an inch. You do have the ability to "cheat" the toilet a smidge forward when installing it, so that might help get it in if it doesn't on the 11-ish inches.
CST744S#01 (the -01 is the color: cotton white) and CST744E#01 each use the same bowl, and the tank is only different in that it has different internals, so, yes, either one would normally fit if you have a full 11 inches.
Yes, the ST743S tank is 1.6gpf. The ST743E tank is 1.28gpf. The CST744S is made up of the C744E bowl and the ST743S tank. The CST744E is made up of the C744E bowl and the ST743E tank. No reason to buy them separately; just get the CST744S or CST744E, depending upon whether you want the 1.28gpf or the 1.6gpf toilet.
Elongated means that the bowl is oval shaped. It's what you want, unless you have some physical obstruction in the room that requires a shorter (round) bowl.
No idea what they mean by "high profile". It's irrelevant, sort of. The CST744S is not a "universal height" or "ADA height" toilet. It is standard height. The CST744SL is the model you want if you want "ADA height".
Close coupled means that the tank sits on the bowl, rather than being mounted on the wall and connected to the bowl with a pipe. All modern two-piece toilets are close-coupled, so it's sort of a useless description.
Open-front is usually something that relates to the seat. An open front seat is like the seats you see in a public lavatory where the part that you would drip pee on is missing; it's more like an upside-down U shape than an O shape. But you buy your own seat for this toilet. It will take any standard manufacturer's seat. The Toto SS114 is a very nice heavy plastic seat, but you can use your old seat or get a Church/Bemis/Mayfair, etc. seat as well.